BACKGROUND: Cardiometabolic multimorbidity (CMM) has emerged as a primary public health challenge, significantly increasing mortality risk and reducing quality of life. Although the metabolic score for visceral fat (METS-VF) and functional limitation are recognized individually as risk factors for cardiometabolic health, the bidirectional relationship between functional limitation and CMM suggests complex underlying mechanisms. However, research investigating the independent and joint effects of METS-VF (representing visceral obesity) and functional limitation on the risk of CMM onset is lacking. This study is aimed at systematically elucidating these associations to provide evidence for targeted interventions. METHODS: This prospective cohort study utilized data from the China Health and Retirement Longitudinal Study (CHARLS). A total of 8140 participants were included in the cross-sectional analysis, and a sub-cohort of 5356 individuals free of CMM at baseline was followed longitudinally. CMM was defined as the coexistence of at least two cardiometabolic diseases: heart disease, diabetes, stroke, or hypertension. Functional limitation was assessed using activities of daily living (ADL) and instrumental ADL (IADL) scales. Multivariable Cox proportional hazards regression and restricted cubic spline (RCS) analysis were employed to evaluate the association between METS-VF, functional limitations, and CMM incidence. RESULTS: During the follow-up period, METS-VF demonstrated a nonlinear positive dose-response relationship with CMM risk. In the longitudinal analysis, participants in the high METS-VF group (defined by the RCS inflection point) exhibited a significantly elevated risk of developing CMM compared to the low-risk group (HR = 1.77, 95% CI: 1.39-2.26) after adjusting for confounders. Continuous functional limitations were also independently associated with incident CMM (HR = 1.12, 95% CI: 1.08-1.16). Notably, a joint effect was observed; participants with both high METS-VF and functional limitations faced the highest risk (HR = 2.43, 95% CI: 1.78-3.31). Receiver operating characteristic (ROC) analysis indicated that the combined model incorporating both factors achieved superior predictive accuracy (AUC = 0.680) compared to single-factor models. CONCLUSION: METS-VF and functional limitations are strong independent predictors of CMM, and their simultaneous presence exerts a significant joint effect on disease risk. The integration of METS-VF and functional assessment into clinical practice can enhance CMM risk stratification and facilitate the early identification of vulnerable high-risk subgroups.